AVM BIOL368 Week 13

Purpose

To fulfill part of the information literacy requirements of this course we will be exploring databases online to fully understand the breath and depth of them. Each student will choose and profile an individual database.

Methods and Results

Part 1: Biological Databases

1. Using Nucleic Acids Research Database Issue Table of Contents 2016 choose a database to profile
2. Answer the following questions:
3. What database did you access? (link to the home page of the database)
   • Withdrawn: A Resource for Withdrawn and Discontinued Drugs
   • [1]
4. What is the purpose of the database?
   • The database was created to provide information about drugs which have been recalled from the market due to safety concerns.
   • [2]
5. What biological information does it contain?
   • This database covers withdrawn and discontinued drugs and protein targets known to interact with said drugs. There are currently 578 drugs contained within the database.
   • [3]
6. What species are covered in the database?
   • This is specifically covering the effects of these drugs on humans.
7. What biological questions can it be used to answer?
   • This database could be used to understand the pathways of certain drugs or the toxicities of particular drugs. If you had questions about the effectiveness of a drug, or were trying to create a new drug you could compare the structure, toxicity type, protein class, chemical makeup and other aspects to the drugs in the database to ensure that the new drug will not have the same effects on the human body.
   • [4]
8. What type (or types) of database is it (sequence, structure model organism, or specialty [what?]; primary or “meta”; curated electronically, manually [in-house], manually [community])?
   • This is a manual, in-house database which was created for the specialty of information on the drug pathways, targets and toxicities.
   • [5]
9. What individual or organization maintains the database?
   • Information for each individual in the team at The Structural Bioinformatics Group can be accessed on the Contact section of the database. The "team" consists of six individuals.
   • [6]
10. What is their funding source(s)?
    • There was no information I could find that provided information on funding of the database.
11. Is there a license agreement or any restrictions on access to the database?
    • Not that I can find, it seems like it is open access to anyone.
12. How often is the database updated? When was the last update?
    • This data base was last updated in September of 2015, this information can be found on the bottom of any page of the website. They have proposed that the database will be updated annually due to the small number of drugs withdrawn per year.
    • to "Conclusions"
13. Are there links to other databases?
    • Yes, within the download tab there are links to ChEMBL, DRUGBANK, e-LEA3D: ChemInformaic Tools and Databases, UniProt, Comparative Toxicogenomics Databases, ConsensusPathDB, World Health Organization, PubMed, and dbSNP.
    • Link
14. Can the information be downloaded? And in what file formats?
    • The drugs in the database can be downloaded based on all drugs, only withdrawn drugs, only discontinued drugs and EMA drugs as SDF files which contain the drug structures and physicochemical properties and structure identifiers.
    • Link
15. Evaluate the “user-friendliness” of the database.
    • I think it is very user-friendly and provided in a very simple, minimal format.
16. Is the Web site well-organized?
    • Yes, it contains tabs for Drugs, Targets, Pathways, Toxicities, Statistics, Help/FAQ, Links/Download, and Contact. The site itself has minimal design but contains all the relevant information needed.
17. Does it have a help section or tutorial?
    • There is a tab for Help/FAQ
    • Section
18. Run a sample query. Do the results make sense?
    • Yes, I searched the withdrawal drug, Sibutramine, and information on when it was approved, discontinued, toxicity type, structure, molecular formula, weight and other information are provided. There are then links to show the drug-target interactions and drug-target PDB complexes.
    • [7]

Part 2: Journal Club

• Please refer to Courtney's page, Journal Club, to view our outline, definitions and questions.

Data and Files

• Slides from DataONE.org
  • DataONE: Why Data Management
• DataONE: Data Sharing
• 
• Schade Journal Club Part I

Acknowledgments

• Template followed from week 14 assignment BIOL368/F16
• Help from our professor, Dr. Dahlquist in class.
• Worked in collaboration with Courtney L. Merriam, Zachary T. Goldstein and Jordan T. Detamore in class as well as outside of class on this assignment. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
• Note: While I recieved assistance from those noted above, this individual journal entry was completed by me and not copied from another source.

Avery Vernon-Moore 18:20, 22 November 2016 (EST)

References

• Rigden, D. J., Fernández-Suárez, X. M., & Galperin, M. Y. (2016). The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. Nucleic acids research, 44(D1), D1-D6. doi: 10.1093/nar/gkv1356
• Siramshetty V.B., Nickel-Seeber J., Omieczynski C., Gohlke B.-O., Drwal M.N., Preissner R.: WITHDRAWN-a resource for withdrawn and discontinued drugs

Nucleic Acids Res (Database issue 2015)

User: Avery_Vernon-Moore

Weekly Assignments:

Assignment 1
Assignment 2
Assignment 3
Assignment 4
Assignment 5
Assignment 6
Assignment 7
Assignment 8
Assignment 9
Assignment 10
Assignment 11
Assignment 12
Assignment 14
Assignment 15

Individual Journals:

"Week 1: Create Wiki Page" 
Individual Journal 2
Individual Journal 3
Individual Journal 4
Individual Journal 5
Individual Journal 6
Individual Journal 7
Individual Journal 8
Individual Journal 9
Individual Journal 10
Individual Journal 11
Individual Journal 12
No Week 13 Assignment
Individual Journal 14
Individual Journal 15

Shared Journals:

Class Journal 1
Class Journal 2
Class Journal 3
Class Journal 4
Class Journal 5
Class Journal 6
Class Journal 7
Class Journal 8
Class Journal 9
Class Journal 10
Class Journal 11
Class Journal 12
Class Journal 14
Class Journal 15